Interpretive Summary: Coccidiosis is an intestinal disease caused by protozoa in the genus Eimeria that inflicts annual losses over. The rapid increase in poultry production in many countries has led to losses due to avian coccidiosis of $ 350 million in the U.S. alone and greater than $ 1 billion worldwide. Coccidiosis control involves either medication of feed with anti-coccidial drugs or vaccination with low doses of live Eimeria oocysts. Effective use of anticoccidial drugs or vaccines requires accurate information on which Eimeria species are present and what drug sensitivity patterns exists in the resident Eimeria population. In the present study, molecular identification techniques were used in conjunction with drug sensitivity testing to assess the role of coccidiosis in various broiler operations. Several important findings are that (1) poultry operations contain more Eimeria species than are present in most live oocyst vaccines, (2) highly virulent strains of Eimeria may be present on low performing farms, (3) drug resistance is lower in operations that use live oocyst vaccines. This information and general approach should be helpful in precise application of avian coccidiosis control strategies.

Technical Abstract:
The purpose of the present study was to evaluate the species distribution and drug sensitivity of Eimeria oocysts isolated from different types of commercial broiler operations. In the first study, litter samples were collected from two groups of broiler farms that differed by means of coccidiosis control (anticoccidial drugs vs. live oocyst vaccines). In the second study, litter samples were collected from broiler farms that differed by location and performance. In study one, vaccine-utilizing (VAC) farms had 2.5 times greater concentrations of oocyst in litter compared to anti-coccidial (ACD) drug-utilizing farms. VAC operations also had greater Eimeria species diversity than ACD-using farms (6 species vs. 4 species) and displayed greater anticoccidial drug sensitivity than ADC farms. In study two, there was no consistent difference in Eimeria oocyst concentrations, species diversity, or drug sensitivity of Eimeria oocysts between high- and low-performing ADC-utilizing farms in two regions. However, low performing farms from both regions contained a highly fecund strain of E. maxima that outcompeted E. acervulina in a subsequent propagation. These studies indicate that PCR-based methods of oocyst typing combined with traditional methods of evaluating anti-coccidial drug sensitivity is useful for characterizing the effect of particular Eimeria species on performance in various types of broiler operations.